Best Compression Technique

[Vergil2501]

So I'm looking to shrink my NGC and Wii collection. I'm not looking for archive quality compression more so compression ratio, looking for what is the best method for removing dummy files and padding and compares games down while still keeping games playable. For NGC I settled on original ISO > GameCube ISO Tool > Dolphin's built in compressor. I have heard stories that some games don't run right after being trimmed like animal crossing (but then again I can't seem to find any sources to prove that is a thing besides what I've read on an emulation wiki). Any suggestions that might work better for NGC or Wii?